Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397257.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_95.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 12062019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 103452 characters in sequence are not A, C, G, or T
File 10 of 26
Found at i:3567482 original size:30 final size:28
Alignment explanation
Indices: 3567309--3567486 Score: 86
Period size: 29 Copynumber: 6.4 Consensus size: 28
3567299 AGGCATTAAA
* *
3567309 GTGTAACAA-A-ATGTTTTTGAATATGGC
1 GTGTAACAACATAT-TTTTTTAACATGGC
* * * *
3567336 GTATAACAATAATATTTTTTCAACATGAC
1 GTGTAACAA-CATATTTTTTTAACATGGC
* * *
3567365 GTGTAATGATAGTATTTTTTTTTCAACATGGC
1 GTGTAA-CA-A-CATATTTTTTT-AACATGGC
*
3567397 GTGTAATAAC--A-TTTTTTAACTATGGC
1 GTGTAACAACATATTTTTTTAAC-ATGGC
* * *
3567423 ATGT---AACATATTTTTGT-ACATAGC
1 GTGTAACAACATATTTTTTTAACATGGC
*
3567447 ATGTAACAACAGTATTTTTTTTAACATGGC
1 GTGTAACAACA-TA-TTTTTTTAACATGGC
3567477 GTGTAACAAC
1 GTGTAACAAC
3567487 TTAACCATGA
Statistics
Matches: 115, Mismatches: 20, Indels: 29
0.70 0.12 0.18
Matches are distributed among these distances:
23 3 0.03
24 8 0.07
25 6 0.05
26 19 0.17
27 12 0.10
28 2 0.02
29 23 0.20
30 19 0.17
31 10 0.09
32 13 0.11
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (28 bp):
GTGTAACAACATATTTTTTTAACATGGC
Found at i:3567502 original size:21 final size:21
Alignment explanation
Indices: 3567467--3567562 Score: 81
Period size: 21 Copynumber: 4.5 Consensus size: 21
3567457 AGTATTTTTT
*
3567467 TTAA-CATGGCGTGTAACAAC
1 TTAACCATGACGTGTAACAAC
* *
3567487 TTAACCATGACATGTAACATATTT
1 TTAACCATGACGTGTAACA-A--C
*
3567511 TTATA-CATGGCGTGTAACAAC
1 TTA-ACCATGACGTGTAACAAC
*
3567532 TTAACCATGGCGTGTAACAA-
1 TTAACCATGACGTGTAACAAC
3567552 TCTAACCATGA
1 T-TAACCATGA
3567563 TATATCACAT
Statistics
Matches: 62, Mismatches: 7, Indels: 13
0.76 0.09 0.16
Matches are distributed among these distances:
20 6 0.10
21 38 0.61
22 1 0.02
23 1 0.02
24 15 0.24
25 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (21 bp):
TTAACCATGACGTGTAACAAC
Found at i:3567512 original size:75 final size:78
Alignment explanation
Indices: 3567375--3567531 Score: 203
Period size: 75 Copynumber: 2.0 Consensus size: 78
3567365 GTGTAATGAT
* * * *
3567375 AGTATTTTTTTTTCAACATGGCGTGTAATAACATTTTTTAACTATGGCATGTAACATATTTTTGT
1 AGTATTTTTTTTTCAACATGGCGTGTAACAAC----TTTAACCATGACATGTAACATATTTTTAT
3567440 ACATAGCATGTAACAAC
62 ACATAGCATGTAACAAC
3567457 AGTA-TTTTTTTT-AACATGGCGTGTAACAAC-TTAACCATGACATGTAACATATTTTTATACAT
1 AGTATTTTTTTTTCAACATGGCGTGTAACAACTTTAACCATGACATGTAACATATTTTTATACAT
* *
3567519 GGCGTGTAACAAC
66 AGCATGTAACAAC
3567532 TTAACCATGG
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
75 40 0.58
80 17 0.25
81 8 0.12
82 4 0.06
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (78 bp):
AGTATTTTTTTTTCAACATGGCGTGTAACAACTTTAACCATGACATGTAACATATTTTTATACAT
AGCATGTAACAAC
Found at i:3567525 original size:45 final size:44
Alignment explanation
Indices: 3567464--3567550 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 44
3567454 AACAGTATTT
3567464 TTTTTAACATGGCGTGTAACAACTTAACCATGACATGTAACATA
1 TTTTTAACATGGCGTGTAACAACTTAACCATGACATGTAACATA
* *
3567508 TTTTTATACATGGCGTGTAACAACTTAACCATGGCGTGTAACA
1 TTTTTA-ACATGGCGTGTAACAACTTAACCATGACATGTAACA
3567551 ATCTAACCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 6 0.15
45 34 0.85
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Consensus pattern (44 bp):
TTTTTAACATGGCGTGTAACAACTTAACCATGACATGTAACATA
Found at i:3567526 original size:24 final size:24
Alignment explanation
Indices: 3567403--3567529 Score: 77
Period size: 24 Copynumber: 5.2 Consensus size: 24
3567393 TGGCGTGTAA
3567403 TAACAT-TTTTTA-ACTATGGCATG
1 TAACATATTTTTATAC-ATGGCATG
* *
3567426 TAACATATTTTTGTACATAGCATG
1 TAACATATTTTTATACATGGCATG
* *
3567450 TAACAACAGTATTTTTTTTAACATGGCGTG
1 T---AACA-TA-TTTTTAT-ACATGGCATG
* *
3567480 TAACA-A--CTTA-ACCATGACATG
1 TAACATATTTTTATA-CATGGCATG
*
3567501 TAACATATTTTTATACATGGCGTG
1 TAACATATTTTTATACATGGCATG
3567525 TAACA
1 TAACA
3567530 ACTTAACCAT
Statistics
Matches: 79, Mismatches: 12, Indels: 25
0.68 0.10 0.22
Matches are distributed among these distances:
20 1 0.01
21 12 0.15
22 3 0.04
23 6 0.08
24 28 0.35
25 4 0.05
27 8 0.10
28 2 0.03
29 6 0.08
30 9 0.11
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (24 bp):
TAACATATTTTTATACATGGCATG
Found at i:3567548 original size:66 final size:66
Alignment explanation
Indices: 3567467--3567661 Score: 196
Period size: 66 Copynumber: 3.0 Consensus size: 66
3567457 AGTATTTTTT
* *
3567467 TTAA-CATGGCGTGTAACAA-CTTAACCATGACATGTAACATATTTTTATACATGGCGTGTAACA
1 TTAACCATGGCGTGTAACAATC-TAACCATGACATATAACATATTTTTATACATGACGTGTAACA
3567530 AC
65 AC
* * * * *
3567532 TTAACCATGGCGTGTAACAATCTAACCATGATATATCACATGTTTTTGTATATGACGTGTAACAA
1 TTAACCATGGCGTGTAACAATCTAACCATGACATATAACATATTTTTATACATGACGTGTAACAA
3567597 C
66 C
* * * * * * ** * * * *
3567598 CTAACCATGGCATGTAATAACCAAATCATGATGTATCACATGTTTTTATATATGACGTATAACA
1 TTAACCATGGCGTGTAACAATCTAACCATGACATATAACATATTTTTATACATGACGTGTAACA
3567662 TGTTTTTGTA
Statistics
Matches: 112, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
65 4 0.04
66 107 0.96
67 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.32
Consensus pattern (66 bp):
TTAACCATGGCGTGTAACAATCTAACCATGACATATAACATATTTTTATACATGACGTGTAACAA
C
Found at i:3569223 original size:15 final size:15
Alignment explanation
Indices: 3569203--3569268 Score: 71
Period size: 15 Copynumber: 4.4 Consensus size: 15
3569193 GTTATCTTTT
3569203 CAACAATCATATTCC
1 CAACAATCATATTCC
*
3569218 CAACAATCATATAT-T
1 CAACAATCATAT-TCC
* * *
3569233 TAGCAATTATATTCC
1 CAACAATCATATTCC
*
3569248 CAACAATCACATTCC
1 CAACAATCATATTCC
3569263 CAACAA
1 CAACAA
3569269 AATACCCAAC
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
14 1 0.03
15 38 0.95
16 1 0.03
ACGTcount: A:0.42, C:0.29, G:0.02, T:0.27
Consensus pattern (15 bp):
CAACAATCATATTCC
Found at i:3571941 original size:14 final size:13
Alignment explanation
Indices: 3571902--3571943 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
3571892 TGATTGGCCT
3571902 AAGAGAAAGAAAA
1 AAGAGAAAGAAAA
*
3571915 ATAGTGAAA-AAAA
1 A-AGAGAAAGAAAA
3571928 AAGGAGAAAGAAAA
1 AA-GAGAAAGAAAA
3571942 AA
1 AA
3571944 AGTATTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
12 1 0.04
13 11 0.46
14 12 0.50
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (13 bp):
AAGAGAAAGAAAA
Found at i:3572480 original size:28 final size:28
Alignment explanation
Indices: 3572435--3572503 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
3572425 TAAATAATAA
* *
3572435 AAACATATAACAAATAAATAAATTACACC
1 AAACATA-AATAAGTAAATAAATTACACC
* * *
3572464 AAATATAAATAAGTAAATACATTACATC
1 AAACATAAATAAGTAAATAAATTACACC
3572492 AAACATAAATAA
1 AAACATAAATAA
3572504 AATTTTAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 28 0.82
29 6 0.18
ACGTcount: A:0.62, C:0.13, G:0.01, T:0.23
Consensus pattern (28 bp):
AAACATAAATAAGTAAATAAATTACACC
Found at i:3575010 original size:36 final size:36
Alignment explanation
Indices: 3574928--3575010 Score: 100
Period size: 36 Copynumber: 2.3 Consensus size: 36
3574918 AACAAACGAT
* *
3574928 AATT-ACAAACAACAATTCACAACTGATTAATCCAA
1 AATTCACAAATAACAATTCACAACTGAATAATCCAA
*
3574963 AATTTCA-AAATAACAATTCACAACT-AATGATCCAA
1 AA-TTCACAAATAACAATTCACAACTGAATAATCCAA
3574998 GAATTCACAAATA
1 -AATTCACAAATA
3575011 TATTTACACA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
35 14 0.34
36 26 0.63
37 1 0.02
ACGTcount: A:0.52, C:0.20, G:0.04, T:0.24
Consensus pattern (36 bp):
AATTCACAAATAACAATTCACAACTGAATAATCCAA
Found at i:3575054 original size:16 final size:16
Alignment explanation
Indices: 3575033--3575070 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3575023 ATAAACAAAG
*
3575033 ATAAAATAATA-ATAAA
1 ATAAAACAATAGAT-AA
3575049 ATAAAACAATAGATAA
1 ATAAAACAATAGATAA
3575065 ATAAAA
1 ATAAAA
3575071 GGAAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (16 bp):
ATAAAACAATAGATAA
Found at i:3578913 original size:23 final size:23
Alignment explanation
Indices: 3578887--3578963 Score: 109
Period size: 23 Copynumber: 3.3 Consensus size: 23
3578877 CTAAATCACA
3578887 CAATGCCTTACTAACTAGTCATG
1 CAATGCCTTACTAACTAGTCATG
*
3578910 CAATGCCTTACTAACTAGTCATA
1 CAATGCCTTACTAACTAGTCATG
* * * *
3578933 CAATGCCGTATTAACAAGTGATG
1 CAATGCCTTACTAACTAGTCATG
3578956 CAATGCCT
1 CAATGCCT
3578964 ATCAACCAGT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (23 bp):
CAATGCCTTACTAACTAGTCATG
Found at i:3578991 original size:23 final size:22
Alignment explanation
Indices: 3578955--3579000 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
3578945 AACAAGTGAT
*
3578955 GCAATGCCTATCAACCAGTCAC
1 GCAATGCATATCAACCAGTCAC
3578977 GCAATGTCATATCAACCAGTCAC
1 GCAATG-CATATCAACCAGTCAC
3579000 G
1 G
3579001 TAATACTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.33, C:0.33, G:0.15, T:0.20
Consensus pattern (22 bp):
GCAATGCATATCAACCAGTCAC
Found at i:3581723 original size:25 final size:25
Alignment explanation
Indices: 3581694--3581750 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
3581684 AATTGTTAAT
*
3581694 AATATTAATCTTCATGCAATAAATA
1 AATATTAATCTTCATACAATAAATA
* *
3581719 AATATTAATCTTTATATAATAAATA
1 AATATTAATCTTCATACAATAAATA
*
3581744 AAGATTA
1 AATATTA
3581751 GTTTAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.39
Consensus pattern (25 bp):
AATATTAATCTTCATACAATAAATA
Found at i:3583596 original size:49 final size:49
Alignment explanation
Indices: 3583524--3583622 Score: 144
Period size: 49 Copynumber: 2.0 Consensus size: 49
3583514 ATATATGAGT
* * * **
3583524 TAACATGTAAATCCGCATAAATCACGAATATTTTTGTGCCATGAACAAG
1 TAACATGTAAATCCACATAAATCACAAATATATTTGTGCCAAAAACAAG
*
3583573 TAACATGTAAATCCATATAAATCACAAATATATTTGTGCCAAAAACAAG
1 TAACATGTAAATCCACATAAATCACAAATATATTTGTGCCAAAAACAAG
3583622 T
1 T
3583623 TGATATTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.28
Consensus pattern (49 bp):
TAACATGTAAATCCACATAAATCACAAATATATTTGTGCCAAAAACAAG
Found at i:3585472 original size:11 final size:11
Alignment explanation
Indices: 3585456--3585481 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3585446 CGGAGAATCT
3585456 CTTCTTCCTTC
1 CTTCTTCCTTC
3585467 CTTCTTCCTTC
1 CTTCTTCCTTC
3585478 CTTC
1 CTTC
3585482 ACTCCTCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (11 bp):
CTTCTTCCTTC
Found at i:3587721 original size:4 final size:4
Alignment explanation
Indices: 3587712--3587742 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
3587702 TGATGTTATA
3587712 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
3587743 TCATTTTAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:3591256 original size:2 final size:2
Alignment explanation
Indices: 3591249--3591278 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3591239 ACCAATTCAT
*
3591249 TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3591279 AAAACTCCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:3603289 original size:20 final size:21
Alignment explanation
Indices: 3603255--3603296 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
3603245 TTAGGTTTTT
3603255 TAAAATAATAATAATAATAAA
1 TAAAATAATAATAATAATAAA
*
3603276 TAAAA-AATAGTAATAATAAA
1 TAAAATAATAATAATAATAAA
3603296 T
1 T
3603297 TAGAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
TAAAATAATAATAATAATAAA
Found at i:3605258 original size:39 final size:40
Alignment explanation
Indices: 3605182--3605262 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
3605172 TTAGCCATTA
**
3605182 TTCACCTTAATGGGGTTTTCTAACCTTGCCAAGATTGGTG
1 TTCACCTTAATGGGGTTTTCTAACCTCACCAAGATTGGTG
*
3605222 TTCACCTTAGTGGGGTTTT-TAACCTCACCACA-ATTGGTG
1 TTCACCTTAATGGGGTTTTCTAACCTCACCA-AGATTGGTG
3605261 TT
1 TT
3605263 TTCACAATGC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
39 18 0.49
40 19 0.51
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (40 bp):
TTCACCTTAATGGGGTTTTCTAACCTCACCAAGATTGGTG
Found at i:3608987 original size:21 final size:21
Alignment explanation
Indices: 3608961--3609031 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
3608951 TTGCGCCTAA
** *
3608961 TATCAAGATTTTGAAATTAGG
1 TATCAAGATTTTGAAACCAAG
*
3608982 TATCAAGACTTTGAAACCAAG
1 TATCAAGATTTTGAAACCAAG
* *
3609003 TATTAAGATTTTGAAACAAAG
1 TATCAAGATTTTGAAACCAAG
3609024 TATCAAGA
1 TATCAAGA
3609032 CTCTGTGAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (21 bp):
TATCAAGATTTTGAAACCAAG
Found at i:3610709 original size:59 final size:60
Alignment explanation
Indices: 3610599--3610730 Score: 160
Period size: 59 Copynumber: 2.2 Consensus size: 60
3610589 AAAGAAAAAC
* * * *
3610599 CTTTAAGCATTTTGAACATTTTATAGTGATTTGTGATACACGAAGACAAACCTTAGAGCG
1 CTTTGAGCATTTTGAACATTTTAGAGTGATTTGTGATACACGAAGAAAAACCTTAGAGCA
* * *
3610659 CTTTGAGCATTTT-AAGCATTTTAGAGTG-TTTTTGATACAGGAAGAAAAACCTTTGAGCA
1 CTTTGAGCATTTTGAA-CATTTTAGAGTGATTTGTGATACACGAAGAAAAACCTTAGAGCA
* *
3610718 TTTTGAGTATTTT
1 CTTTGAGCATTTT
3610731 TTGCCAAGTA
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
59 39 0.63
60 23 0.37
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (60 bp):
CTTTGAGCATTTTGAACATTTTAGAGTGATTTGTGATACACGAAGAAAAACCTTAGAGCA
Found at i:3610785 original size:22 final size:21
Alignment explanation
Indices: 3610760--3610814 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 21
3610750 GTTGATTGTA
3610760 TTGTTAAATGAAATA-TGATGT
1 TTGTTAAATGAAATATTGAT-T
* *
3610781 GTTGTTTAA--AATTATTGATT
1 -TTGTTAAATGAAATATTGATT
3610801 TTGTTAAATGAAAT
1 TTGTTAAATGAAAT
3610815 TCAATAGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
19 7 0.27
20 5 0.19
21 7 0.27
22 7 0.27
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.47
Consensus pattern (21 bp):
TTGTTAAATGAAATATTGATT
Found at i:3610876 original size:22 final size:22
Alignment explanation
Indices: 3610851--3610908 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
3610841 TTATGTAATA
* *
3610851 AGTTTTTAGGTATTACGTGACT
1 AGTTTTTAGATATTACATGACT
* *
3610873 AGTTTTTAAACATTACATGACT
1 AGTTTTTAGATATTACATGACT
3610895 AGTTTTTAGATATT
1 AGTTTTTAGATATT
3610909 GCGTAACTGG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.47
Consensus pattern (22 bp):
AGTTTTTAGATATTACATGACT
Found at i:3610937 original size:45 final size:44
Alignment explanation
Indices: 3610851--3610939 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 44
3610841 TTATGTAATA
* *
3610851 AGTTTTTAGGTATTACGTGACTAGTTTTTAAACATTACATGACT
1 AGTTTTTAGATATTACGTAACTAGTTTTTAAACATTACATGACT
* * *
3610895 AGTTTTTAGATATTGCGTAACTGGTTGATTT-AACATTGCATGACT
1 AGTTTTTAGATATTACGTAACTAGTT--TTTAAACATTACATGACT
3610940 GATTGATAGG
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
44 22 0.58
45 13 0.34
46 3 0.08
ACGTcount: A:0.28, C:0.11, G:0.18, T:0.43
Consensus pattern (44 bp):
AGTTTTTAGATATTACGTAACTAGTTTTTAAACATTACATGACT
Found at i:3610998 original size:23 final size:22
Alignment explanation
Indices: 3610971--3611032 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 22
3610961 TAATTTTTAA
3610971 GTATTACGTGACTGGTTCATATG
1 GTATTACGTGACTGGTTCATA-G
* * *
3610994 GTATTACGTGATTGATTGATAG
1 GTATTACGTGACTGGTTCATAG
*
3611016 GTATTGCGTGACTGGTT
1 GTATTACGTGACTGGTT
3611033 TTTGGACATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 15 0.45
23 18 0.55
ACGTcount: A:0.21, C:0.10, G:0.29, T:0.40
Consensus pattern (22 bp):
GTATTACGTGACTGGTTCATAG
Found at i:3611188 original size:22 final size:23
Alignment explanation
Indices: 3611153--3611203 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
3611143 CAATAATAAG
* *
3611153 TCACATTACTTAAAAATCAGT-A
1 TCACAATACCTAAAAATCAGTGA
3611175 TCACAATACCTAAAAATCAGTGA
1 TCACAATACCTAAAAATCAGTGA
3611198 -CACAAT
1 TCACAAT
3611204 GTTTAAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.47, C:0.22, G:0.06, T:0.25
Consensus pattern (23 bp):
TCACAATACCTAAAAATCAGTGA
Found at i:3613004 original size:12 final size:13
Alignment explanation
Indices: 3612977--3613004 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3612967 AATAAGGAGA
3612977 TTTTTCCTGTATT
1 TTTTTCCTGTATT
3612990 TTTTTCCTGTATT
1 TTTTTCCTGTATT
3613003 TT
1 TT
3613005 ATTAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.14, G:0.07, T:0.71
Consensus pattern (13 bp):
TTTTTCCTGTATT
Found at i:3615818 original size:82 final size:79
Alignment explanation
Indices: 3615684--3615841 Score: 235
Period size: 82 Copynumber: 2.0 Consensus size: 79
3615674 GTCTGTGGTA
* * *
3615684 TGCAGGACATGAGTGCTTCCCTGCACCCCTTAATGCAATGTTGACAACTAGTTTTGCCTTGTGTA
1 TGCAGGACATGAGTGATCCCCTGCACCCCTTAATGCAATGTTGACAACTAGTTATGCCTTGTGTA
*
3615749 TGCTTTGAGTGTGG
66 TGCCTTGAGTGTGG
* *
3615763 TGCAGGACATGAGTCGATCCCCCTTGTACCCCTTAATGCAATGTTGACAACTAGTTATGTCTTGT
1 TGCAGGACATGAGT-GAT-CCCC-TGCACCCCTTAATGCAATGTTGACAACTAGTTATGCCTTGT
3615828 GTATGCCTTGAGTG
63 GTATGCCTTGAGTG
3615842 CAGTTTGTCC
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
79 14 0.20
80 2 0.03
81 3 0.04
82 51 0.73
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (79 bp):
TGCAGGACATGAGTGATCCCCTGCACCCCTTAATGCAATGTTGACAACTAGTTATGCCTTGTGTA
TGCCTTGAGTGTGG
Found at i:3624156 original size:35 final size:36
Alignment explanation
Indices: 3624117--3624205 Score: 103
Period size: 35 Copynumber: 2.6 Consensus size: 36
3624107 TACTTCATAC
*
3624117 AGAATAACTA-AATCAAGTGAAGTAATACTTCACGT
1 AGAATAACTAGAATCAAGTGAAATAATACTTCACGT
* * * *
3624152 AGAATAATTAGAA-CAAATGAAATACTATTTCACGT
1 AGAATAACTAGAATCAAGTGAAATAATACTTCACGT
*
3624187 AGAACAACTAGAAT-AAGTG
1 AGAATAACTAGAATCAAGTG
3624206 TAGCACTATT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
35 42 0.95
36 2 0.05
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.25
Consensus pattern (36 bp):
AGAATAACTAGAATCAAGTGAAATAATACTTCACGT
Found at i:3634397 original size:30 final size:30
Alignment explanation
Indices: 3634356--3634417 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
3634346 ACCATTCATC
* **
3634356 ATAAGGACTTATTTAACTTGAAACAAAAAT
1 ATAAAGACTTATTTAACTAAAAACAAAAAT
* *
3634386 ATAAAGACTTATTTGACTAAAAATAAAAAT
1 ATAAAGACTTATTTAACTAAAAACAAAAAT
3634416 AT
1 AT
3634418 TAGAGTTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (30 bp):
ATAAAGACTTATTTAACTAAAAACAAAAAT
Found at i:3652716 original size:34 final size:33
Alignment explanation
Indices: 3652618--3652784 Score: 138
Period size: 34 Copynumber: 4.9 Consensus size: 33
3652608 GGGTTTGTGG
* *
3652618 TTGAGTCTTGTAAAAACCAATGTTGAAGGGTTTTAC
1 TTGA-TCTTGTAAAAAGCATTG-TG-AGGGTTTTAC
** * * *
3652654 TTGATCTTGTGAAAAAATATTATAAGGGTTTCAC
1 TTGATCTTGT-AAAAAGCATTGTGAGGGTTTTAC
*
3652688 TTGATCTTGTGAAAAAGCATTGTGAGGGTTTTGC
1 TTGATCTTGT-AAAAAGCATTGTGAGGGTTTTAC
*** * * *
3652722 TTGATCCCAT-AAAAGTATTGTAAGGGTTTTGC
1 TTGATCTTGTAAAAAGCATTGTGAGGGTTTTAC
*
3652754 TTGATCTCGTAAAAAGCTATTGTGAGGGTTT
1 TTGATCTTGTAAAAAGC-ATTGTGAGGGTTT
3652785 CGTTTGATCC
Statistics
Matches: 107, Mismatches: 21, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
32 28 0.26
33 5 0.05
34 56 0.52
35 7 0.07
36 11 0.10
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (33 bp):
TTGATCTTGTAAAAAGCATTGTGAGGGTTTTAC
Found at i:3652758 original size:66 final size:66
Alignment explanation
Indices: 3652666--3652802 Score: 195
Period size: 66 Copynumber: 2.1 Consensus size: 66
3652656 GATCTTGTGA
* *
3652666 AAAAATATTATAAGGGTTTCACTTGATCTTGTGAAAAAGC-ATTGTGAGGGTTTTGCTTGATCCC
1 AAAAATATTATAAGGGTTTCACTTGATCTCGT-AAAAAGCTATTGTGAGGGTTTCGCTTGATCCC
3652730 AT
65 AT
* * ** *
3652732 AAAAGTATTGTAAGGGTTTTGCTTGATCTCGTAAAAAGCTATTGTGAGGGTTTCGTTTGATCCCA
1 AAAAATATTATAAGGGTTTCACTTGATCTCGTAAAAAGCTATTGTGAGGGTTTCGCTTGATCCCA
3652797 T
66 T
3652798 AAAAA
1 AAAAA
3652803 GGTTATGTCT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
65 7 0.11
66 55 0.89
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.36
Consensus pattern (66 bp):
AAAAATATTATAAGGGTTTCACTTGATCTCGTAAAAAGCTATTGTGAGGGTTTCGCTTGATCCCA
T
Found at i:3652792 original size:34 final size:34
Alignment explanation
Indices: 3652699--3652803 Score: 135
Period size: 32 Copynumber: 3.2 Consensus size: 34
3652689 TGATCTTGTG
*
3652699 AAAAAGC-ATTGTGAGGGTTTTGCTTGATCCCAT
1 AAAAAGCTATTGTGAGGGTTTCGCTTGATCCCAT
* * * *
3652732 -AAAAG-TATTGTAAGGGTTTTGCTTGATCTCGT
1 AAAAAGCTATTGTGAGGGTTTCGCTTGATCCCAT
*
3652764 AAAAAGCTATTGTGAGGGTTTCGTTTGATCCCAT
1 AAAAAGCTATTGTGAGGGTTTCGCTTGATCCCAT
3652798 AAAAAG
1 AAAAAG
3652804 GTTATGTCTC
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
32 28 0.46
33 5 0.08
34 28 0.46
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.34
Consensus pattern (34 bp):
AAAAAGCTATTGTGAGGGTTTCGCTTGATCCCAT
Found at i:3658940 original size:36 final size:34
Alignment explanation
Indices: 3658900--3658979 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 34
3658890 TTGAGTCCAT
* ** *
3658900 AAAAACCATTGTCGAAAGGTTTTGCTTGATCTTATG
1 AAAAAACATTGT--AAAGGTTTCCCTTGATCTCATG
* *
3658936 AAAAAGCATTGTAAGGGTTTCCCTTGATCTCATG
1 AAAAAACATTGTAAAGGTTTCCCTTGATCTCATG
3658970 AAAAAACATT
1 AAAAAACATT
3658980 ATGAGTGTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 27 0.71
36 11 0.29
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (34 bp):
AAAAAACATTGTAAAGGTTTCCCTTGATCTCATG
Found at i:3658990 original size:34 final size:34
Alignment explanation
Indices: 3658924--3658990 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
3658914 AAAGGTTTTG
* * *
3658924 CTTGATCTTATGAAAAAGCATTGTAAGGGTTTCC
1 CTTGATCTCATGAAAAAACATTATAAGGGTTTCC
* *
3658958 CTTGATCTCATGAAAAAACATTATGAGTGTTTC
1 CTTGATCTCATGAAAAAACATTATAAGGGTTTC
3658991 ACTTAATCCC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (34 bp):
CTTGATCTCATGAAAAAACATTATAAGGGTTTCC
Found at i:3677404 original size:15 final size:17
Alignment explanation
Indices: 3677384--3677415 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
3677374 CCTTTGATAT
3677384 ATCATG-AGCA-TGATC
1 ATCATGAAGCATTGATC
3677399 ATCATGAAGCATTGATC
1 ATCATGAAGCATTGATC
3677416 TAGACTCCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (17 bp):
ATCATGAAGCATTGATC
Found at i:3678001 original size:28 final size:28
Alignment explanation
Indices: 3677966--3678129 Score: 148
Period size: 28 Copynumber: 5.7 Consensus size: 28
3677956 ATGACAGCTT
* *
3677966 AAACATGTTTGTATTAATTTAGACAAGA
1 AAACATATTTGTCTTAATTTAGACAAGA
* * *
3677994 AAACATGTTTAGTCTTATTTTAGATAAGA
1 AAACATATTT-GTCTTAATTTAGACAAGA
* * *
3678023 AAATATTTTTGTCTTAATTTAACACAAGAA
1 AAACATATTTGTCTTAATTT-AGACAAG-A
* * *
3678053 AAATATATTTGTCTTAATCTAGACAAAA
1 AAACATATTTGTCTTAATTTAGACAAGA
* * *
3678081 AAACATATTTATCTCAATTTAGATAAGA
1 AAACATATTTGTCTTAATTTAGACAAGA
*
3678109 TAACATATTTTTGTCTTAATT
1 AAACATA--TTTGTCTTAATT
3678130 AAAGACAAAA
Statistics
Matches: 110, Mismatches: 21, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
28 48 0.44
29 33 0.30
30 29 0.26
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.40
Consensus pattern (28 bp):
AAACATATTTGTCTTAATTTAGACAAGA
Found at i:3678016 original size:29 final size:29
Alignment explanation
Indices: 3677966--3678129 Score: 138
Period size: 29 Copynumber: 5.7 Consensus size: 29
3677956 ATGACAGCTT
* *
3677966 AAACATGTTT-GTATTAATTTAGACAAGA
1 AAACATATTTAGTCTTAATTTAGACAAGA
* * *
3677994 AAACATGTTTAGTCTTATTTTAGATAAGA
1 AAACATATTTAGTCTTAATTTAGACAAGA
* * *
3678023 AAATAT-TTTTGTCTTAATTTAACACAAGA
1 AAACATATTTAGTCTTAATTT-AGACAAGA
* * *
3678052 AAA-ATATATTTGTCTTAATCTAGACAAAA
1 AAACATAT-TTAGTCTTAATTTAGACAAGA
* *
3678081 AAACATATTTA-TCTCAATTTAGATAAGA
1 AAACATATTTAGTCTTAATTTAGACAAGA
* *
3678109 TAACATATTTTTGTCTTAATT
1 AAACATA-TTTAGTCTTAATT
3678130 AAAGACAAAA
Statistics
Matches: 110, Mismatches: 19, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
28 43 0.39
29 44 0.40
30 23 0.21
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.40
Consensus pattern (29 bp):
AAACATATTTAGTCTTAATTTAGACAAGA
Found at i:3678310 original size:17 final size:18
Alignment explanation
Indices: 3678285--3678318 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3678275 ATAAAATAAA
3678285 AGTTATTATTTAATAAGG
1 AGTTATTATTTAATAAGG
*
3678303 AGTT-TTATTTCATAAG
1 AGTTATTATTTAATAAG
3678319 AACTTTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (18 bp):
AGTTATTATTTAATAAGG
Found at i:3679710 original size:11 final size:11
Alignment explanation
Indices: 3679694--3679728 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
3679684 CTATGTTTTT
3679694 AAATTAATAAA
1 AAATTAATAAA
*
3679705 AAATTAATTAA
1 AAATTAATAAA
3679716 AAATTAATAAA
1 AAATTAATAAA
3679727 AA
1 AA
3679729 TAATATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
AAATTAATAAA
Found at i:3679729 original size:21 final size:21
Alignment explanation
Indices: 3679694--3679760 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
3679684 CTATGTTTTT
3679694 AAATTAATAAAAAATTAATTAA
1 AAATTAAT-AAAAATTAATTAA
3679716 AAATTAATAAAAA-TAATATAA
1 AAATTAATAAAAATTAAT-TAA
* * * *
3679737 TAATT-TTTAAAATTAATAAA
1 AAATTAATAAAAATTAATTAA
3679757 AAAT
1 AAAT
3679761 AAAATTTCAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 14 0.37
21 16 0.42
22 8 0.21
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AAATTAATAAAAATTAATTAA
Found at i:3685006 original size:15 final size:14
Alignment explanation
Indices: 3684967--3685007 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
3684957 AAATTTTGTC
3684967 CTATAACACCTTATA
1 CTATAACA-CTTATA
*
3684982 CTATAACACTTCATG
1 CTATAACACTT-ATA
3684997 CTATAACACTT
1 CTATAACACTT
3685008 TACGCCGCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 3 0.12
15 21 0.88
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (14 bp):
CTATAACACTTATA
Found at i:3685069 original size:15 final size:15
Alignment explanation
Indices: 3685049--3685078 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3685039 AGATATTAAT
3685049 GCCTTAAACAGTAAC
1 GCCTTAAACAGTAAC
*
3685064 GCCTTAAATAGTAAC
1 GCCTTAAACAGTAAC
3685079 ACTTTAGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.23
Consensus pattern (15 bp):
GCCTTAAACAGTAAC
Found at i:3685089 original size:15 final size:15
Alignment explanation
Indices: 3685050--3685092 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
3685040 GATATTAATG
* *
3685050 CCTTAAACAGTAACG
1 CCTTAAATAGTAACA
3685065 CCTTAAATAGTAACA
1 CCTTAAATAGTAACA
* *
3685080 CTTTAGATAGTAA
1 CCTTAAATAGTAA
3685093 TATGCTATTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.28
Consensus pattern (15 bp):
CCTTAAATAGTAACA
Found at i:3685356 original size:66 final size:64
Alignment explanation
Indices: 3685239--3685363 Score: 160
Period size: 66 Copynumber: 1.9 Consensus size: 64
3685229 AATGTTTTTC
* * ***
3685239 ATAAAAACCTTGATTCTATGTCTTATAAATAACTGAGAGTAAAATTCTATCTTGTGTGTAATAG
1 ATAAAAACCTTGATTCTATGACCTATAAATAACTGAGAGTAAAAGAATATCTTGTGTGTAATAG
** *
3685303 ATAAAAACCTTGATTTTCTATGACCTATAAATAGTTGAGAGTAATAGAATATCTTGTGTGT
1 ATAAAAACCTTGA--TTCTATGACCTATAAATAACTGAGAGTAAAAGAATATCTTGTGTGT
3685364 GGTATCGTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
64 13 0.25
66 38 0.75
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (64 bp):
ATAAAAACCTTGATTCTATGACCTATAAATAACTGAGAGTAAAAGAATATCTTGTGTGTAATAG
Found at i:3701301 original size:2 final size:2
Alignment explanation
Indices: 3701288--3701322 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3701278 TTACGTAGTG
*
3701288 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3701323 CATAAAACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3705374 original size:16 final size:16
Alignment explanation
Indices: 3705344--3705373 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3705334 TCAAAATTTA
3705344 GATTTTGATTGTTTTG
1 GATTTTGATTGTTTTG
3705360 GATTTTGATT-TTTT
1 GATTTTGATTGTTTT
3705374 TTGATATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.13, C:0.00, G:0.20, T:0.67
Consensus pattern (16 bp):
GATTTTGATTGTTTTG
Found at i:3706431 original size:21 final size:22
Alignment explanation
Indices: 3706407--3706457 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
3706397 AAAGCAGAAT
*
3706407 AGAATAAGTTTTGA-AG-AAAAA
1 AGAA-AAGTTTTAAGAGAAAAAA
*
3706428 AGAAACGTTTTAAGAGAAAAAA
1 AGAAAAGTTTTAAGAGAAAAAA
3706450 AGAAAAGT
1 AGAAAAGT
3706458 GTACCTGGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 7 0.28
21 6 0.24
22 12 0.48
ACGTcount: A:0.59, C:0.02, G:0.20, T:0.20
Consensus pattern (22 bp):
AGAAAAGTTTTAAGAGAAAAAA
Found at i:3709724 original size:21 final size:22
Alignment explanation
Indices: 3709689--3709732 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
3709679 CTCTTAAAGT
3709689 AATTTAAAATAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
*
3709711 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
3709732 A
1 A
3709733 TTAATCACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (22 bp):
AATTTAAAATAAAATAACTTAA
Found at i:3715785 original size:18 final size:20
Alignment explanation
Indices: 3715744--3715789 Score: 69
Period size: 18 Copynumber: 2.4 Consensus size: 20
3715734 CAAAAGAAAA
3715744 AAAAAGAATAAGTGTTGAAC
1 AAAAAGAATAAGTGTTGAAC
*
3715764 AAAAAGAA-AAGT-TTGAAG
1 AAAAAGAATAAGTGTTGAAC
3715782 AAAAAGAA
1 AAAAAGAA
3715790 GAAAGGTGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 13 0.52
19 4 0.16
20 8 0.32
ACGTcount: A:0.63, C:0.02, G:0.20, T:0.15
Consensus pattern (20 bp):
AAAAAGAATAAGTGTTGAAC
Found at i:3719820 original size:17 final size:17
Alignment explanation
Indices: 3719798--3719831 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3719788 CCTATAAAAG
3719798 TAATAAACT-AACTTAAA
1 TAAT-AACTAAACTTAAA
3719815 TAATAACTAAACTTAAA
1 TAATAACTAAACTTAAA
3719832 GCAAAATACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (17 bp):
TAATAACTAAACTTAAA
Found at i:3721264 original size:1 final size:1
Alignment explanation
Indices: 3721258--3721291 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
3721248 TTAAAGTCTT
3721258 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
3721292 TTCAAATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:3732658 original size:36 final size:37
Alignment explanation
Indices: 3732618--3732702 Score: 118
Period size: 36 Copynumber: 2.3 Consensus size: 37
3732608 TGTGTAAATA
*
3732618 TGTTTGTGAATTCTTGGATCAATTAGTTGTGAATTG-
1 TGTTTGTGAATTCTTGGATCAATCAGTTGTGAATTGT
* * *
3732654 TGTTTTTGAATTGTTGGATTAATCAGTTGTGAATTGT
1 TGTTTGTGAATTCTTGGATCAATCAGTTGTGAATTGT
*
3732691 TGTTTGTAAATT
1 TGTTTGTGAATT
3732703 GTTGTTTGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 32 0.76
37 10 0.24
ACGTcount: A:0.22, C:0.04, G:0.24, T:0.51
Consensus pattern (37 bp):
TGTTTGTGAATTCTTGGATCAATCAGTTGTGAATTGT
Found at i:3732702 original size:14 final size:14
Alignment explanation
Indices: 3732680--3732711 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3732670 GATTAATCAG
*
3732680 TTGTGAATTGTTGT
1 TTGTAAATTGTTGT
3732694 TTGTAAATTGTTGT
1 TTGTAAATTGTTGT
3732708 TTGT
1 TTGT
3732712 TGGTCTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.25, T:0.59
Consensus pattern (14 bp):
TTGTAAATTGTTGT
Found at i:3735154 original size:28 final size:28
Alignment explanation
Indices: 3735123--3735191 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 28
3735113 ATTTAAAATT
3735123 TTATTTATGTTT-GATGTAATGTATTTGC
1 TTATTTATGTTTAG-TGTAATGTATTTGC
* *
3735151 TTATTTATGTTTAGTGTAATTTATTTGT
1 TTATTTATGTTTAGTGTAATGTATTTGC
*
3735179 TTGTTATATGTTT
1 TTATT-TATGTTT
3735192 TTATTATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 28 0.78
29 8 0.22
ACGTcount: A:0.20, C:0.01, G:0.16, T:0.62
Consensus pattern (28 bp):
TTATTTATGTTTAGTGTAATGTATTTGC
Found at i:3736497 original size:21 final size:21
Alignment explanation
Indices: 3736451--3736505 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
3736441 ATAATAAAAT
*
3736451 ATTAATTAATTAATGTTACTA
1 ATTAATCAATTAATGTTACTA
* *
3736472 CTTAATCAATTAAT-TTATTGA
1 ATTAATCAATTAATGTTACT-A
*
3736493 ATTAATCGATTAA
1 ATTAATCAATTAA
3736506 ATGCCTTTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 4 0.14
21 24 0.86
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.45
Consensus pattern (21 bp):
ATTAATCAATTAATGTTACTA
Found at i:3740395 original size:20 final size:20
Alignment explanation
Indices: 3740372--3740436 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
3740362 TAATATTAAA
3740372 ATTTTAAATAAAATAATAAT
1 ATTTTAAATAAAATAATAAT
* *
3740392 ATTTTAAAATATTAATGAGTAA-
1 ATTTT-AAATA-AAAT-AATAAT
* *
3740414 ATTATAAATAAAATATTAAT
1 ATTTTAAATAAAATAATAAT
3740434 ATT
1 ATT
3740437 GAAATTGAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
19 4 0.11
20 11 0.31
21 10 0.28
22 7 0.19
23 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
ATTTTAAATAAAATAATAAT
Found at i:3740623 original size:27 final size:26
Alignment explanation
Indices: 3740593--3740649 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
3740583 TATTAATACT
*
3740593 TAAATGATTAATCATTAACATTTTAAA
1 TAAATGATAAATCATTAACA-TTTAAA
* * *
3740620 TAAATTATAAATTATTAATATTTAAA
1 TAAATGATAAATCATTAACATTTAAA
3740646 -AAAT
1 TAAAT
3740650 AATATAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 4 0.15
26 6 0.23
27 16 0.62
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (26 bp):
TAAATGATAAATCATTAACATTTAAA
Found at i:3748761 original size:34 final size:34
Alignment explanation
Indices: 3748723--3748911 Score: 98
Period size: 28 Copynumber: 5.9 Consensus size: 34
3748713 ATGCTAAGGT
*
3748723 CAAAGTTTCAACACTAGATGTTACATGCCAAAAC
1 CAAAGCTTCAACACTAGATGTTACATGCCAAAAC
* *
3748757 CAAAGCTT------TAGATGTTACATGCTAAGAC
1 CAAAGCTTCAACACTAGATGTTACATGCCAAAAC
* * * ** *
3748785 TAAAGCTTCAGCACTAGATGTTATACACCAAAGC
1 CAAAGCTTCAACACTAGATGTTACATGCCAAAAC
* * ***
3748819 CAAAG---C-AGA--AGATGTTACACGCCAATGT
1 CAAAGCTTCAACACTAGATGTTACATGCCAAAAC
* * * *
3748847 CAAAGCTTCAATACTAGATGTTAC-TACCAAGAG
1 CAAAGCTTCAACACTAGATGTTACATGCCAAAAC
* * *
3748880 CAAAGTTTCAGCACCAGATGTTACATGCCAAA
1 CAAAGCTTCAACACTAGATGTTACATGCCAAA
3748912 GCTTCCTTCT
Statistics
Matches: 113, Mismatches: 29, Indels: 26
0.67 0.17 0.15
Matches are distributed among these distances:
28 45 0.40
30 1 0.01
31 2 0.02
32 2 0.02
33 24 0.21
34 39 0.35
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (34 bp):
CAAAGCTTCAACACTAGATGTTACATGCCAAAAC
Found at i:3748773 original size:62 final size:61
Alignment explanation
Indices: 3748704--3748870 Score: 181
Period size: 62 Copynumber: 2.7 Consensus size: 61
3748694 CTTCAATAAC
* * ** ***
3748704 AGATGTTATATGCTAAGGTCAAAGTTTCAACACTAGATGTTACATGCCAAAACCAAAGCTTT
1 AGATGTTACATGCTAA-GTCAAAGCTTCAACACTAGATGTTACACACCAAAACCAAAGCAGA
* * * *
3748766 AGATGTTACATGCTAAGACTAAAGCTTCAGCACTAGATGTTATACACCAAAGCCAAAGCAGA
1 AGATGTTACATGCTAAGTC-AAAGCTTCAACACTAGATGTTACACACCAAAACCAAAGCAGA
* * *
3748828 AGATGTTACACGCCAATGTCAAAGCTTCAATACTAGATGTTAC
1 AGATGTTACATGCTAA-GTCAAAGCTTCAACACTAGATGTTAC
3748871 TACCAAGAGC
Statistics
Matches: 86, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
61 2 0.02
62 82 0.95
63 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.26
Consensus pattern (61 bp):
AGATGTTACATGCTAAGTCAAAGCTTCAACACTAGATGTTACACACCAAAACCAAAGCAGA
Found at i:3757033 original size:54 final size:53
Alignment explanation
Indices: 3756975--3757412 Score: 206
Period size: 54 Copynumber: 8.1 Consensus size: 53
3756965 TTTTCCTACA
* *
3756975 TTCCTTCTTAAACTTAAGAGTTGGAATTCTAGACAGGCTTTGATTCTTCAAATC
1 TTCCTTCTTAGACTTAAG-GTTGGAATTCTAGAGAGGCTTTGATTCTTCAAATC
* * * * *
3757029 TTCCTTCTT-GAACTTGCAGGTTGGAAATCTGGAGAGGCTTTGGTTCTTCAAAATA
1 TTCCTTCTTAG-ACTT-AAGGTTGGAATTCTAGAGAGGCTTTGATTCTTC-AAATC
** * * * * * * * *
3757084 TTAATTCTTGGATTTGTAGGTTGAAAATCTAGAGAGGCTTTGATTCTTTAGATT
1 TTCCTTCTTAGACTT-AAGGTTGGAATTCTAGAGAGGCTTTGATTCTTCAAATC
*** * * * * *
3757138 TTCCTTCTTAGACTTGTTCGTTGAAATTCTAGTGAAGCTTTCATTCTTCAAAATA
1 TTCCTTCTTAGACTT-AAGGTTGGAATTCTAGAGAGGCTTTGATTCTTC-AAATC
* * * * *
3757193 TTGCTTCTTAGATTTGTAGGTTGAAATTCTTA-AAAGGCTTT-AGTTCTTCAAATC
1 TTCCTTCTTAGACTT-AAGGTTGGAATTC-TAGAGAGGCTTTGA-TTCTTCAAATC
* * ** * * *
3757247 TTTCTTTTTAGACTTGTGGGTTGGAATT-TTGAATAGGCTTTGGTTCTTCAAATC
1 TTCCTTCTTAGACTT-AAGGTTGGAATTCTAG-AGAGGCTTTGATTCTTCAAATC
* * * * * * * *
3757301 TTTCTTTTTAGACTTATGGGTTGGAATT-TTGAATAGGCCTTGGTTCTTCAAAATT
1 TTCCTTCTTAGACTTA-AGGTTGGAATTCTAG-AGAGGCTTTGATTCTTC-AAATC
** * * * *
3757356 TTCCTTCTGGGA-TTAATAGGTTAGAAATCTAAAGAAGCTTT-ATTTCTTCAAATC
1 TTCCTTCTTAGACTT-A-AGGTTGGAATTCTAGAGAGGCTTTGA-TTCTTCAAATC
3757410 TTC
1 TTC
3757413 TTTTTTGGAT
Statistics
Matches: 306, Mismatches: 63, Indels: 30
0.77 0.16 0.08
Matches are distributed among these distances:
52 1 0.00
54 182 0.59
55 119 0.39
56 4 0.01
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (53 bp):
TTCCTTCTTAGACTTAAGGTTGGAATTCTAGAGAGGCTTTGATTCTTCAAATC
Found at i:3757112 original size:55 final size:55
Alignment explanation
Indices: 3756974--3757269 Score: 228
Period size: 54 Copynumber: 5.4 Consensus size: 55
3756964 TTTTTCCTAC
* * * * *
3756974 ATTCCTTCTTAAACTT-AAGAGTTGGAATTCTAGACAGGCTTTGATTCTTC-AAAT
1 ATTCCTTCTTAGACTTGTAG-GTTGAAAATCTAGAGAGGCTTTGATTCTTCAAAAT
* * * * *
3757028 CTTCCTTCTT-GAACTTGCAGGTTGGAAATCTGGAGAGGCTTTGGTTCTTCAAAAT
1 ATTCCTTCTTAG-ACTTGTAGGTTGAAAATCTAGAGAGGCTTTGATTCTTCAAAAT
** * * * *
3757083 ATTAATTCTTGGATTTGTAGGTTGAAAATCTAGAGAGGCTTTGATTCTT-TAGAT
1 ATTCCTTCTTAGACTTGTAGGTTGAAAATCTAGAGAGGCTTTGATTCTTCAAAAT
* ** * * * *
3757137 TTTCCTTCTTAGACTTGTTCGTTGAAATTCTAGTGAAGCTTTCATTCTTCAAAAT
1 ATTCCTTCTTAGACTTGTAGGTTGAAAATCTAGAGAGGCTTTGATTCTTCAAAAT
* * * *
3757192 ATTGCTTCTTAGATTTGTAGGTTGAAATTCTTA-AAAGGCTTT-AGTTCTTC-AAAT
1 ATTCCTTCTTAGACTTGTAGGTTGAAAATC-TAGAGAGGCTTTGA-TTCTTCAAAAT
* * * *
3757246 CTTTCTTTTTAGACTTGTGGGTTG
1 ATTCCTTCTTAGACTTGTAGGTTG
3757270 GAATTTTGAA
Statistics
Matches: 192, Mismatches: 43, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
54 104 0.54
55 85 0.44
56 3 0.02
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.43
Consensus pattern (55 bp):
ATTCCTTCTTAGACTTGTAGGTTGAAAATCTAGAGAGGCTTTGATTCTTCAAAAT
Found at i:3757122 original size:109 final size:109
Alignment explanation
Indices: 3757002--3757298 Score: 314
Period size: 109 Copynumber: 2.7 Consensus size: 109
3756992 GAGTTGGAAT
* *
3757002 TCTAGACAGGCTTTGATTCTTCAAATCTTCCTTCTT-GAACTTGCAGGTTGGAAATCTGGAGAGG
1 TCTAGAAAGGCTTTGATTCTTCAAATCTTCCTTCTTAG-ACTTGTAGGTTGGAAATCTGGAGAGG
*
3757066 CTTTGGTTCTTCAAAATATTAATTCTTGGATTTGTAGGTTGAAAA
65 CTTTGGTTCTTCAAAATATTAATTCTTAGATTTGTAGGTTGAAAA
* * * * ** * * *
3757111 TCTAGAGAGGCTTTGATTCTTTAGATTTTCCTTCTTAGACTTGTTCGTT-GAAATTCTAGTGAAG
1 TCTAGAAAGGCTTTGATTCTTCAAATCTTCCTTCTTAGACTTGTAGGTTGGAAA-TCTGGAGAGG
** ** *
3757175 CTTTCATTCTTCAAAATATTGCTTCTTAGATTTGTAGGTTGAAAT
65 CTTTGGTTCTTCAAAATATTAATTCTTAGATTTGTAGGTTGAAAA
* * * * * * *
3757220 TCTTA-AAAGGCTTT-AGTTCTTCAAATCTTTCTTTTTAGACTTGTGGGTTGGAATTTTGAATAG
1 TC-TAGAAAGGCTTTGA-TTCTTCAAATCTTCCTTCTTAGACTTGTAGGTTGGAAATCTGGAGAG
3757283 GCTTTGGTTCTTCAAA
64 GCTTTGGTTCTTCAAA
3757299 TCTTTCTTTT
Statistics
Matches: 150, Mismatches: 33, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
108 5 0.03
109 139 0.93
110 6 0.04
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (109 bp):
TCTAGAAAGGCTTTGATTCTTCAAATCTTCCTTCTTAGACTTGTAGGTTGGAAATCTGGAGAGGC
TTTGGTTCTTCAAAATATTAATTCTTAGATTTGTAGGTTGAAAA
Found at i:3757994 original size:30 final size:30
Alignment explanation
Indices: 3757959--3758138 Score: 159
Period size: 30 Copynumber: 5.9 Consensus size: 30
3757949 CATAATTTCC
3757959 CTATCTTTTCAAGGCTTAAG-TAGAACCTC-
1 CTATCTTTTCAAGGC-TAAGATAGAACCTCT
* * *
3757988 CTTATCTTGTCAAGGCTAAGGTAGAACCTTT
1 C-TATCTTTTCAAGGCTAAGATAGAACCTCT
* * * *
3758019 CTATCTATTCAAGGCCAAGATAAAATCTC-
1 CTATCTTTTCAAGGCTAAGATAGAACCTCT
* * *
3758048 CTTAATTTTTTTCAAGGCTTAGATAGAACATCT
1 C-T-A-TCTTTTCAAGGCTAAGATAGAACCTCT
* * *
3758081 CTATCTTTTCAAGACTGAGATAGAACTTCT
1 CTATCTTTTCAAGGCTAAGATAGAACCTCT
* *
3758111 CTATATTTTCAAGGCTAAGATAAAACCT
1 CTATCTTTTCAAGGCTAAGATAGAACCT
3758139 TTAATTACTA
Statistics
Matches: 119, Mismatches: 25, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
29 6 0.05
30 89 0.75
31 3 0.03
32 20 0.17
33 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (30 bp):
CTATCTTTTCAAGGCTAAGATAGAACCTCT
Found at i:3758086 original size:92 final size:92
Alignment explanation
Indices: 3757964--3758135 Score: 224
Period size: 92 Copynumber: 1.9 Consensus size: 92
3757954 TTTCCCTATC
* * * *
3757964 TTTTCAAGGCTTAAGTAGAACCTCCTTATCTTGTCAAGGCTAAGGTAGAACCTT-TCTATCTATT
1 TTTTCAAGGCTTAAGTAGAACATCCTTATCTTGTCAAGACTAAGATAGAA-CTTCTCTATATATT
3758028 CAAGGCCAAGATAAAATCTCCTTAATTT
65 CAAGGCCAAGATAAAATCTCCTTAATTT
* * *
3758056 TTTTCAAGGCTT-AGATAGAACAT-CTCTATCTTTTCAAGACTGAGATAGAACTTCTCTATATTT
1 TTTTCAAGGCTTAAG-TAGAACATCCT-TATCTTGTCAAGACTAAGATAGAACTTCTCTATATAT
*
3758119 TCAAGGCTAAGATAAAA
64 TCAAGGCCAAGATAAAA
3758136 CCTTTAATTA
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
91 7 0.10
92 62 0.90
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (92 bp):
TTTTCAAGGCTTAAGTAGAACATCCTTATCTTGTCAAGACTAAGATAGAACTTCTCTATATATTC
AAGGCCAAGATAAAATCTCCTTAATTT
Found at i:3759263 original size:57 final size:54
Alignment explanation
Indices: 3759186--3759293 Score: 153
Period size: 57 Copynumber: 1.9 Consensus size: 54
3759176 AGTTTTGATT
3759186 TGACCAAATTTACATCTTATCTCTAAATTATCTTAATTAATTTAGAGATAAATTGAA
1 TGACCAAATTTACATCTTATCTCTAAATTATC-TAA--AATTTAGAGATAAATTGAA
** * *
3759243 TGACCAAATTTTGATTTTATCTCTAAATTATCTAAATTTTAGAGATAAATT
1 TGACCAAATTTACATCTTATCTCTAAATTATCTAAAATTTAGAGATAAATT
3759294 ATATGACTGA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
54 15 0.32
56 3 0.06
57 29 0.62
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (54 bp):
TGACCAAATTTACATCTTATCTCTAAATTATCTAAAATTTAGAGATAAATTGAA
Found at i:3760015 original size:13 final size:13
Alignment explanation
Indices: 3759993--3760024 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3759983 TTCTACCAAG
*
3759993 GATGCCTAAATAA
1 GATGCTTAAATAA
3760006 GATGCTTAAATAA
1 GATGCTTAAATAA
3760019 GATGCT
1 GATGCT
3760025 ATTAGGCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (13 bp):
GATGCTTAAATAA
Found at i:3774303 original size:20 final size:20
Alignment explanation
Indices: 3774278--3774354 Score: 127
Period size: 20 Copynumber: 3.9 Consensus size: 20
3774268 TCCTTCAGTG
* * *
3774278 ATGTATTGATACATTTGTCA
1 ATGTATCGATACATCTGGCA
3774298 ATGTATCGATACATCTGGCA
1 ATGTATCGATACATCTGGCA
3774318 ATGTATCGATACATCTGGCA
1 ATGTATCGATACATCTGGCA
3774338 ATGTATCGATACATCTG
1 ATGTATCGATACATCTG
3774355 TCTTAATTTC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATCTGGCA
Found at i:3778786 original size:32 final size:32
Alignment explanation
Indices: 3778745--3778809 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
3778735 TTTAGTACTT
* *
3778745 AGCAAAGGATTTTGGTGCAACTCTCTGTGGGA
1 AGCAAAGGATTTTGGTACAACTCTCTATGGGA
3778777 AGCAAAGGATTTTGGTACAACTCTCTATGGGA
1 AGCAAAGGATTTTGGTACAACTCTCTATGGGA
3778809 A
1 A
3778810 TGATACTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (32 bp):
AGCAAAGGATTTTGGTACAACTCTCTATGGGA
Found at i:3780117 original size:17 final size:18
Alignment explanation
Indices: 3780092--3780131 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
3780082 ATTTTCGACT
* *
3780092 TTTACATTT-GTTTTTAA
1 TTTAAATTTCGTTTTAAA
3780109 TTTAAATTTCGTTTTAAA
1 TTTAAATTTCGTTTTAAA
3780127 TTTAA
1 TTTAA
3780132 TTAACGAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (18 bp):
TTTAAATTTCGTTTTAAA
Found at i:3791561 original size:55 final size:55
Alignment explanation
Indices: 3791477--3791595 Score: 211
Period size: 55 Copynumber: 2.2 Consensus size: 55
3791467 CCTAATGCTA
*
3791477 ATTGGCTTGATCCATATCATCAAAGTTGTAAAGCAATAGCTGAGTATTAGTGCAG
1 ATTGGCTTGATCCATATCATCAAAGTTGTAAAGCAATAGCTGAGTATCAGTGCAG
* *
3791532 ATTGGCTTGATCCATATTATCAAAGTTGTAAAGCAGTAGCTGAGTATCAGTGCAG
1 ATTGGCTTGATCCATATCATCAAAGTTGTAAAGCAATAGCTGAGTATCAGTGCAG
3791587 ATTGGCTTG
1 ATTGGCTTG
3791596 CTTGAATAAT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 61 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (55 bp):
ATTGGCTTGATCCATATCATCAAAGTTGTAAAGCAATAGCTGAGTATCAGTGCAG
Found at i:3793960 original size:71 final size:71
Alignment explanation
Indices: 3793807--3793989 Score: 203
Period size: 71 Copynumber: 2.6 Consensus size: 71
3793797 CAAGCATTTG
* * * * * *
3793807 ATTAAAATTGTTCAATTAAG---TTGTGCCTAATTAATTAAATTGTTTAACTACGTCATTTGGCC
1 ATTAAAATTATTTAATTAAGTTATTGGGCCTAATTGATTAAATTGTTTAACTAAGTCATTTGACC
*
3793869 TAATTG
66 TAATTA
* **
3793875 ATTAAAATTATTTAATTAAGTTATTGGGCCTAATTGATTAACATTGTTTAATTAAGTTGTTTGAC
1 ATTAAAATTATTTAATTAAGTTATTGGGCCTAATTGATTAA-ATTGTTTAACTAAGTCATTTGAC
*
3793940 TTAATTA
65 CTAATTA
* * *
3793947 ATT-AAATTTTTTAATTAAGTTATTGGACGTAATTGATTAAATT
1 ATTAAAATTATTTAATTAAGTTATTGGGCCTAATTGATTAAATT
3793990 AAACAATTAA
Statistics
Matches: 97, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
68 18 0.19
70 3 0.03
71 50 0.52
72 26 0.27
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.46
Consensus pattern (71 bp):
ATTAAAATTATTTAATTAAGTTATTGGGCCTAATTGATTAAATTGTTTAACTAAGTCATTTGACC
TAATTA
Found at i:3793967 original size:35 final size:35
Alignment explanation
Indices: 3793804--3793989 Score: 182
Period size: 36 Copynumber: 5.3 Consensus size: 35
3793794 TCTCAAGCAT
* *
3793804 TTGATTAAAATTGTTCAATTAAGTT-GT-G-CCTAA
1 TTGATT-AAATTGTTTAATTAAGTTATTGGACCTAA
* * * *
3793837 TTAATTAAATTGTTTAACTACGTCATTTGG-CCTAA
1 TTGATTAAATTGTTTAATTAAGTTA-TTGGACCTAA
* *
3793872 TTGATTAAAATTATTTAATTAAGTTATTGGGCCTAA
1 TTGATT-AAATTGTTTAATTAAGTTATTGGACCTAA
* * *
3793908 TTGATTAACATTGTTTAATTAAGTTGTTTGACTTAA
1 TTGATTAA-ATTGTTTAATTAAGTTATTGGACCTAA
* * *
3793944 TTAATTAAATTTTTTAATTAAGTTATTGGACGTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGACCTAA
3793979 TTGATTAAATT
1 TTGATTAAATT
3793990 AAACAATTAA
Statistics
Matches: 125, Mismatches: 22, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
32 14 0.11
33 5 0.04
34 1 0.01
35 50 0.40
36 55 0.44
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.46
Consensus pattern (35 bp):
TTGATTAAATTGTTTAATTAAGTTATTGGACCTAA
Found at i:3798830 original size:317 final size:317
Alignment explanation
Indices: 3798236--3798863 Score: 1044
Period size: 317 Copynumber: 2.0 Consensus size: 317
3798226 CAAAGAGAAG
* * * *
3798236 ATATTTTCTATCAATGTGGCAAACTTGGGCATTAGAGAAGGAACTGTAAAGAGTAACTAGCTACT
1 ATATTTGCCATCAATGTGGCAAAATTAGGCATTAGAGAAGGAACTGTAAAGAGTAACTAGCTACT
* *
3798301 ATGAACAAGAAAAGAAGCTTATTGAAGTTTCTGATTTAGGTATCATTTGTTAAATAATTCTACTT
66 ATGAACAAGAAAAAAAGCTTATTGAAGTTTCTGATTTAGGTATCATTTGCTAAATAATTCTACTT
* *
3798366 TATATATTAAGGGTATATGATACCTCAAAATTGGTTCTCATATGTTTGACATATTACAAGGACCA
131 TATATATTAAAGGTATATGATACCTCAAAATTGGTTCTCATATGTTTGACATATTACAAGAACCA
*
3798431 AAGATAAAGATGAGTAGGATATTAGCTAAAGAAGTGACCACATGGATGGACTACCTAAGCATTAA
196 AAGATAAAGATGAGTAGAATATTAGCTAAAGAAGTGACCACATGGATGGACTACCTAAGCATTAA
* *
3798496 ATGCTACATTGGATGGTTGCACTTCTATTTATCTTGACATGTTGGACAATTAACTTC
261 ATGCTACATTGGATGGTTACACTCCTATTTATCTTGACATGTTGGACAATTAACTTC
* *
3798553 ATATTTGCCATCATTGTGGCAAAATTAGGCATTAGAGAAGGAATTGTAAAGAGT-ACTTAGCTAC
1 ATATTTGCCATCAATGTGGCAAAATTAGGCATTAGAGAAGGAACTGTAAAGAGTAAC-TAGCTAC
* *
3798617 TGTGAGCAAGAAAAAAAGCTTATTGAAGTTTCTGATTTAGGTATCATTTGCTAAATAATTCTACT
65 TATGAACAAGAAAAAAAGCTTATTGAAGTTTCTGATTTAGGTATCATTTGCTAAATAATTCTACT
*
3798682 TTATATATTAAAGGTATATGATACCTCAAAATTGG-TGTCATATGTTTGACATATTACAAGAACC
130 TTATATATTAAAGGTATATGATACCTCAAAATTGGTTCTCATATGTTTGACATATTACAAGAACC
* *
3798746 AAAGATAAAGATGAGTAGAATATTGGCTAAAGAGGTGACCACATGGATGGACTACCTAAAGCATT
195 AAAGATAAAGATGAGTAGAATATTAGCTAAAGAAGTGACCACATGGATGGACTACCT-AAGCATT
* *
3798811 AAATGCTACATTTGATGGTTACACTCCTATTTATCTTGACATGTTGGATAATT
259 AAATGCTACATTGGATGGTTACACTCCTATTTATCTTGACATGTTGGACAATT
3798864 TATTTGGATG
Statistics
Matches: 289, Mismatches: 20, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
316 83 0.29
317 206 0.71
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.33
Consensus pattern (317 bp):
ATATTTGCCATCAATGTGGCAAAATTAGGCATTAGAGAAGGAACTGTAAAGAGTAACTAGCTACT
ATGAACAAGAAAAAAAGCTTATTGAAGTTTCTGATTTAGGTATCATTTGCTAAATAATTCTACTT
TATATATTAAAGGTATATGATACCTCAAAATTGGTTCTCATATGTTTGACATATTACAAGAACCA
AAGATAAAGATGAGTAGAATATTAGCTAAAGAAGTGACCACATGGATGGACTACCTAAGCATTAA
ATGCTACATTGGATGGTTACACTCCTATTTATCTTGACATGTTGGACAATTAACTTC
Found at i:3800232 original size:14 final size:14
Alignment explanation
Indices: 3800192--3800234 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
3800182 TAATGCATAG
3800192 AAATTAGTATATTTT
1 AAATTAGT-TATTTT
* *
3800207 -ATTTAATTATTTT
1 AAATTAGTTATTTT
3800220 AAATTAGTTATTTT
1 AAATTAGTTATTTT
3800234 A
1 A
3800235 GATGAGTCAG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (14 bp):
AAATTAGTTATTTT
Found at i:3801033 original size:21 final size:21
Alignment explanation
Indices: 3801009--3801076 Score: 93
Period size: 21 Copynumber: 3.2 Consensus size: 21
3800999 GTTCATGCAA
3801009 TTCATGACAAAGATAGATGCC
1 TTCATGACAAAGATAGATGCC
* *
3801030 TTCATGACCAAGACAGATGCC
1 TTCATGACAAAGATAGATGCC
3801051 TTCATGACAAAGACT-GATGCC
1 TTCATGACAAAGA-TAGATGCC
*
3801072 ATCAT
1 TTCAT
3801077 TCAAAGTCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (21 bp):
TTCATGACAAAGATAGATGCC
Found at i:3801588 original size:18 final size:17
Alignment explanation
Indices: 3801556--3801591 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
3801546 TTCGAAACTC
3801556 TTATTTTTTAGTTATTT
1 TTATTTTTTAGTTATTT
*
3801573 TTATTTATTTATTTATTT
1 TTATTT-TTTAGTTATTT
3801591 T
1 T
3801592 CATTAATTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (17 bp):
TTATTTTTTAGTTATTT
Found at i:3803004 original size:3 final size:3
Alignment explanation
Indices: 3802996--3803045 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
3802986 ACTTTATCTC
* *
3802996 TAG TAG TAG TAG TAC TAG TTA- TAG TAG TAG TAC TAG TTA- TAG TAG
1 TAG TAG TAG TAG TAG TAG -TAG TAG TAG TAG TAG TAG -TAG TAG TAG
3803041 TAG TA
1 TAG TA
3803046 CTAATAACTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 4 0.10
3 31 0.79
4 4 0.10
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (3 bp):
TAG
Found at i:3803022 original size:18 final size:18
Alignment explanation
Indices: 3802999--3803048 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
3802989 TTATCTCTAG
3802999 TAGTAGTAGTACTAGTTA
1 TAGTAGTAGTACTAGTTA
3803017 TAGTAGTAGTACTAGTTA
1 TAGTAGTAGTACTAGTTA
3803035 TAGTAGTAGTACTA
1 TAGTAGTAGTACTA
3803049 ATAACTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (18 bp):
TAGTAGTAGTACTAGTTA
Found at i:3810674 original size:70 final size:71
Alignment explanation
Indices: 3810597--3810741 Score: 213
Period size: 70 Copynumber: 2.1 Consensus size: 71
3810587 CTAGCAAGAT
* * *
3810597 TTGAACTTACATTAACAAAGGCATGAGACTTTTAA-AAATATCCTTTAACTACTT-CACCAAGGA
1 TTGAACTTACATTAACAAAGGCATGAGACTTTAAACAAATATCCTTCAACCA-TTACACCAAGGA
*
3810660 AGCATCC
65 ACCATCC
* *
3810667 TTGAACTTGCATTAACAAAGTCATGAGACTTTAAACAAATATCCTTCAACCATTACACCAAGGAA
1 TTGAACTTACATTAACAAAGGCATGAGACTTTAAACAAATATCCTTCAACCATTACACCAAGGAA
3810732 CCATCC
66 CCATCC
3810738 TTGA
1 TTGA
3810742 GATGAGAGTG
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
70 34 0.51
71 33 0.49
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.28
Consensus pattern (71 bp):
TTGAACTTACATTAACAAAGGCATGAGACTTTAAACAAATATCCTTCAACCATTACACCAAGGAA
CCATCC
Found at i:3811861 original size:28 final size:28
Alignment explanation
Indices: 3811829--3811887 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
3811819 CGCTATGTCA
3811829 GCTATGACAAGAAAGATGAAAGCAATTG
1 GCTATGACAAGAAAGATGAAAGCAATTG
3811857 GCTATGACAAGAAAGATGAAAGCAATTG
1 GCTATGACAAGAAAGATGAAAGCAATTG
3811885 GCT
1 GCT
3811888 GTGATCTCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.44, C:0.12, G:0.25, T:0.19
Consensus pattern (28 bp):
GCTATGACAAGAAAGATGAAAGCAATTG
Found at i:3813650 original size:49 final size:49
Alignment explanation
Indices: 3813578--3813680 Score: 197
Period size: 49 Copynumber: 2.1 Consensus size: 49
3813568 GGGCTAACTG
*
3813578 AGATGGAATCTCGTTATATTGATTTTCTAAAAGATGACTTCCCAAGCAT
1 AGATGGAATCTCATTATATTGATTTTCTAAAAGATGACTTCCCAAGCAT
3813627 AGATGGAATCTCATTATATTGATTTTCTAAAAGATGACTTCCCAAGCAT
1 AGATGGAATCTCATTATATTGATTTTCTAAAAGATGACTTCCCAAGCAT
3813676 AGATG
1 AGATG
3813681 AGGTTAAAGA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Consensus pattern (49 bp):
AGATGGAATCTCATTATATTGATTTTCTAAAAGATGACTTCCCAAGCAT
Found at i:3816693 original size:15 final size:14
Alignment explanation
Indices: 3816673--3816741 Score: 54
Period size: 15 Copynumber: 4.9 Consensus size: 14
3816663 TAGGATATAA
3816673 ATTTAAATTTAATTT
1 ATTTAAATTTAA-TT
*
3816688 ATTTAAATTTAAAT
1 ATTTAAATTTAATT
*
3816702 A-AT-AA-TTAATT
1 ATTTAAATTTAATT
3816713 ACTTTTAAATTTAATTT
1 A--TTTAAATTTAA-TT
*
3816730 GTTTAAATTTAA
1 ATTTAAATTTAA
3816742 AAGTAATATC
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
11 6 0.14
12 2 0.05
13 1 0.02
14 3 0.07
15 25 0.58
16 4 0.09
17 2 0.05
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (14 bp):
ATTTAAATTTAATT
Found at i:3816696 original size:21 final size:21
Alignment explanation
Indices: 3816670--3816742 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
3816660 AGATAGGATA
3816670 TAAATTTAAATTTAATTTATT
1 TAAATTTAAATTTAATTTATT
* *
3816691 TAAATTTAAATAATAA-TTAAT
1 TAAATTTAAAT-TTAATTTATT
** *
3816712 TACTTTTAAATTTAATTTGTT
1 TAAATTTAAATTTAATTTATT
3816733 TAAATTTAAA
1 TAAATTTAAA
3816743 AGTAATATCC
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 3 0.07
21 35 0.85
22 3 0.07
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (21 bp):
TAAATTTAAATTTAATTTATT
Found at i:3817940 original size:18 final size:18
Alignment explanation
Indices: 3817917--3817970 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
3817907 TCATTCATTC
3817917 GGAAGCATTCGAAGATTG
1 GGAAGCATTCGAAGATTG
*
3817935 GGAAGCATTTGAAGATTG
1 GGAAGCATTCGAAGATTG
3817953 GGAAGCATTCGAAGATTG
1 GGAAGCATTCGAAGATTG
3817971 AGAGCATTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.33, C:0.09, G:0.33, T:0.24
Consensus pattern (18 bp):
GGAAGCATTCGAAGATTG
Found at i:3818259 original size:18 final size:18
Alignment explanation
Indices: 3818236--3818271 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3818226 TCATTCATTT
3818236 GGAAGCATTCGAAGATTG
1 GGAAGCATTCGAAGATTG
3818254 GGAAGCATTCGAAGATTG
1 GGAAGCATTCGAAGATTG
3818272 AGAGCATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.33, T:0.22
Consensus pattern (18 bp):
GGAAGCATTCGAAGATTG
Found at i:3818344 original size:23 final size:23
Alignment explanation
Indices: 3818317--3818391 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
3818307 CTGAAGTGAA
**
3818317 GATCAAGTGATGGCGAAGTTCGT
1 GATCAAGTGATAACGAAGTTCGT
*
3818340 GATCAAGCGATAACGAAGTTCGT
1 GATCAAGTGATAACGAAGTTCGT
* *
3818363 GATCAAGTTATCAAC--TGTTCGT
1 GATCAAGTGAT-AACGAAGTTCGT
3818385 GATCAAG
1 GATCAAG
3818392 ATTAAGTCGT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
22 13 0.29
23 29 0.64
24 3 0.07
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.27
Consensus pattern (23 bp):
GATCAAGTGATAACGAAGTTCGT
Found at i:3818434 original size:49 final size:49
Alignment explanation
Indices: 3818372--3818471 Score: 164
Period size: 49 Copynumber: 2.0 Consensus size: 49
3818362 TGATCAAGTT
* *
3818372 ATCAACTGTTCGTGATCAAGATTAAGTCGTGAGGACCCTTGAAGCGAAG
1 ATCAACTGTTCGTGATCAAGATTAAGTCGTGAAGACCCTTGAAGAGAAG
* *
3818421 ATCAAGTGTTCGTGATCAAGATTACGTCGTGAAGACCCTTGAAGAGAAG
1 ATCAACTGTTCGTGATCAAGATTAAGTCGTGAAGACCCTTGAAGAGAAG
3818470 AT
1 AT
3818472 TAAGCAAAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (49 bp):
ATCAACTGTTCGTGATCAAGATTAAGTCGTGAAGACCCTTGAAGAGAAG
Found at i:3819636 original size:19 final size:22
Alignment explanation
Indices: 3819608--3819660 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 22
3819598 TTTATAAATT
3819608 TATTGA-ATATATT-AT-ATCA
1 TATTGATATATATTAATAATCA
3819627 TATT-ATATAT-TTAATAATCA
1 TATTGATATATATTAATAATCA
*
3819647 TATTGATATTTATT
1 TATTGATATATATT
3819661 TTAAGATTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 3 0.11
19 10 0.36
20 8 0.29
21 5 0.18
22 2 0.07
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (22 bp):
TATTGATATATATTAATAATCA
Found at i:3825065 original size:33 final size:36
Alignment explanation
Indices: 3824994--3825065 Score: 87
Period size: 39 Copynumber: 2.0 Consensus size: 36
3824984 TAAGTTTGAT
*
3824994 AAATATTAATATTTAACTTAAAATATTAAAAATATTTAA
1 AAATATTAATATTTAACTT---ATATAAAAAATATTTAA
3825033 AAATATTAATATTTAACTT-T-TAAAAAAT-TTTAA
1 AAATATTAATATTTAACTTATATAAAAAATATTTAA
3825066 CTTAAAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
33 5 0.16
34 7 0.22
35 1 0.03
39 19 0.59
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (36 bp):
AAATATTAATATTTAACTTATATAAAAAATATTTAA
Found at i:3827932 original size:16 final size:17
Alignment explanation
Indices: 3827911--3827943 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3827901 AGAAGACTGG
*
3827911 ATAAAATGTTA-CAAAA
1 ATAAAATCTTATCAAAA
3827927 ATAAAATCTTATCAAAA
1 ATAAAATCTTATCAAAA
3827944 TATCTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.61, C:0.09, G:0.03, T:0.27
Consensus pattern (17 bp):
ATAAAATCTTATCAAAA
Found at i:3833389 original size:21 final size:21
Alignment explanation
Indices: 3833351--3833390 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3833341 CACAAAATAG
* *
3833351 AAAGTAAATATGTTTATATTT
1 AAAGTAAATATATATATATTT
*
3833372 AAAGTACATATATATATAT
1 AAAGTAAATATATATATAT
3833391 ATATATATAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (21 bp):
AAAGTAAATATATATATATTT
Found at i:3834085 original size:345 final size:332
Alignment explanation
Indices: 3833426--3834098 Score: 768
Period size: 345 Copynumber: 2.0 Consensus size: 332
3833416 CGCACACATC
* * * ***
3833426 AAAAATATTTTAATATATATAATAGTAGTTATATTTTTTATAAATAAATTTAATATATATAAATA
1 AAAAATATTTTAATATATATAATAGCAATTATATTTCTTATAAATAAACACAATATATATAAATA
* * * * *
3833491 TATATTAAAAGATATTACAAGTTAATTAATAATTATGATTTCCTTAATAATTTTATTAACTACAC
66 TATATTAAAAGACATTACAAGTTAATTAATAATAATGATTTCATGAATAATTTAATTAACTACAC
** * * *
3833556 AAGTTTGTCTTTAATTACATAAAATTAAAAAAAATAACTGAATTTTAGAACTATTCTAATTTCAT
131 AAGTTTGTCTTTAATTACATAAAATTAAAAAAAATAACTGAATTCCAAAACTATTCTAATCTCAA
* * * *
3833621 AACTTCTCTTTAGGTTTATATAAGTTTATATAAACAAAGTTATATATCTTATAATTAATAATTTT
196 AACTTCTCTTTAGATTTATATAAGATTATACAAACAAAGTTATATATATTATAATTAATAATTTT
* * *
3833686 ATAAATTATAATTTTGTAATGTTAATACAAAATAGAAGGTAAACATGATTATATTTAAAGTATAT
261 ATAAATCATAATTTTGTAATGTTAATACAAAATAGAAAGTAAACATGATTATATTAAAAGTATAT
3833751 ATAAACT
326 ATAAACT
* *
3833758 AAAAATATTTTAGTATATATATAATAGCAATTATATTTCTTATAGATTAACACAATATATA-AAC
1 AAAAATATTTTA--ATATATATAATAGCAATTATATTTCTTATAAATAAACACAATATATATAA-
*
3833822 TATATATATTTAAAGACATTACAAGTTAATTAATAATAAT-AGTTTCATGAATTAATTTAATTAA
63 -ATATATATTAAAAGACATTACAAGTTAATTAATAATAATGA-TTTCATGAA-TAATTTAATTAA
* * * * * * *
3833886 TTATATGAA-TTTGT-TCTTAATCT-CATGAAATTAAAAAAAA-ACACTTAGGTTCCAAAATTAT
125 CTACA-CAAGTTTGTCT-TTAAT-TACATAAAATTAAAAAAAATA-ACTGA-ATTCCAAAACTAT
*
3833947 TCTAATCTCAAAAGCTT-TCTTTAAGTATATATATTATAAGATTATACAAACAATGGTATATATA
185 TCTAATCTCAAAA-CTTCTCTTT-AG-AT-T-TA-TATAAGATTATACAAACAA-AGT-TATATA
* * *
3834011 TATTATAATTAATAATTTTATAAGTCATAATTTTTGTAATGTTAATATAAAATAGAAAGTAAATA
242 TATTATAATTAATAATTTTATAAATCATAA-TTTTGTAATGTTAATACAAAATAGAAAGTAAACA
3834076 T-ATTTATATTAAAAGTATATATA
306 TGA-TTATATTAAAAGTATATATA
3834099 TACATATAAT
Statistics
Matches: 283, Mismatches: 37, Indels: 29
0.81 0.11 0.08
Matches are distributed among these distances:
332 12 0.04
333 2 0.01
334 40 0.14
335 45 0.16
336 44 0.16
337 27 0.10
338 5 0.02
339 1 0.00
340 1 0.00
341 2 0.01
342 17 0.06
343 2 0.01
344 34 0.12
345 51 0.18
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (332 bp):
AAAAATATTTTAATATATATAATAGCAATTATATTTCTTATAAATAAACACAATATATATAAATA
TATATTAAAAGACATTACAAGTTAATTAATAATAATGATTTCATGAATAATTTAATTAACTACAC
AAGTTTGTCTTTAATTACATAAAATTAAAAAAAATAACTGAATTCCAAAACTATTCTAATCTCAA
AACTTCTCTTTAGATTTATATAAGATTATACAAACAAAGTTATATATATTATAATTAATAATTTT
ATAAATCATAATTTTGTAATGTTAATACAAAATAGAAAGTAAACATGATTATATTAAAAGTATAT
ATAAACT
Found at i:3834105 original size:21 final size:21
Alignment explanation
Indices: 3834066--3834119 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
3834056 TATAAAATAG
**
3834066 AAAGTAAATATATTTATATTA
1 AAAGTAAATATATACATATTA
*
3834087 AAAGTATATATATACATA-TA
1 AAAGTAAATATATACATATTA
* *
3834107 ATAGTAATTATAT
1 AAAGTAAATATAT
3834120 TCTTTTATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.41
Consensus pattern (21 bp):
AAAGTAAATATATACATATTA
Found at i:3835656 original size:43 final size:43
Alignment explanation
Indices: 3835568--3835649 Score: 164
Period size: 43 Copynumber: 1.9 Consensus size: 43
3835558 TTTGTGTCTA
3835568 TGATATTGTCTTTGGTATTAGATTCACAAAGCTTGTATCCTAG
1 TGATATTGTCTTTGGTATTAGATTCACAAAGCTTGTATCCTAG
3835611 TGATATTGTCTTTGGTATTAGATTCACAAAGCTTGTATC
1 TGATATTGTCTTTGGTATTAGATTCACAAAGCTTGTATC
3835650 GCAGTGAGCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.43
Consensus pattern (43 bp):
TGATATTGTCTTTGGTATTAGATTCACAAAGCTTGTATCCTAG
Found at i:3853025 original size:21 final size:21
Alignment explanation
Indices: 3853000--3853129 Score: 114
Period size: 21 Copynumber: 6.4 Consensus size: 21
3852990 GATCCTACCC
*
3853000 ATATTAATATTTGTAAATAAA
1 ATATTAATATTTATAAATAAA
*
3853021 ATATTAATATTT-TAAAATATTA
1 ATATTAATATTTAT-AAATA-AA
*
3853043 ATGTTAA-A-TTATAAATAAA
1 ATATTAATATTTATAAATAAA
*
3853062 TTATTAATATTTATAAAATAAA
1 ATATTAATATTTAT-AAATAAA
* *
3853084 A-ATAAATATTCAT-AATAAA
1 ATATTAATATTTATAAATAAA
*
3853103 AT-TTAA-A-TTATAAATATA
1 ATATTAATATTTATAAATAAA
3853121 ATATTAATA
1 ATATTAATA
3853130 CTTAAATTAT
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
17 3 0.03
18 8 0.09
19 20 0.23
20 10 0.11
21 33 0.38
22 14 0.16
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (21 bp):
ATATTAATATTTATAAATAAA
Found at i:3853126 original size:59 final size:61
Alignment explanation
Indices: 3853000--3853129 Score: 160
Period size: 59 Copynumber: 2.1 Consensus size: 61
3852990 GATCCTACCC
* * * *
3853000 ATATTAATATTTGTAAATAAAATATTAATATTTTAAAATATTAATGTTAAATTATAAATAA
1 ATATTAATATTTATAAATAAAATATAAATATTTCAAAATATAAATGTTAAATTATAAATAA
*
3853061 ATTATTAATATTTATAAAATAAAA-ATAAATA-TTCATAATA-AAAT-TTAAATTATAAATATA
1 A-TATTAATATTTAT-AAATAAAATATAAATATTTCAAAATATAAATGTTAAATTATAAATA-A
3853121 ATATTAATA
1 ATATTAATA
3853130 CTTAAATTAT
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
59 22 0.36
60 5 0.08
61 8 0.13
62 18 0.30
63 8 0.13
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (61 bp):
ATATTAATATTTATAAATAAAATATAAATATTTCAAAATATAAATGTTAAATTATAAATAA
Found at i:3853260 original size:20 final size:19
Alignment explanation
Indices: 3853202--3853272 Score: 72
Period size: 19 Copynumber: 3.5 Consensus size: 19
3853192 AATAATCATA
*
3853202 ATAATATTTAATTATAAAT
1 ATAATATTAAATTATAAAT
*
3853221 AAAATATTAATATCT-TATAAT
1 ATAATATTAA-AT-TATA-AAT
3853242 ATTAATAATTAAATTATAAAT
1 A-TAAT-ATTAAATTATAAAT
3853263 ATAATATTAA
1 ATAATATTAA
3853273 TATTTAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
19 13 0.30
20 8 0.19
21 10 0.23
22 7 0.16
23 5 0.12
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAATATTAAATTATAAAT
Found at i:3853274 original size:97 final size:97
Alignment explanation
Indices: 3853013--3853306 Score: 319
Period size: 104 Copynumber: 2.9 Consensus size: 97
3853003 TTAATATTTG
* *
3853013 TAAATAAAATATTAATATTTTAAAATATTAATGTTAAATTATAAATA-AATTATTAATATTTATA
1 TAAATAAAATATTAATATCTT-AAATATTAATATTAAATTATAAATATAATTATTAATATTTA-A
* * *
3853077 AAATAAAAATAAATATTCATAATAAAATTTAAATTA
64 AAA-ATAAA-AAATAATCATAATAATATTTAAATTA
* * * *
3853113 TAAATATAATATTAATA-CTTAAATTATCAGTCATTAATATTTTAACTAATATTAAATTATTAAT
1 TAAATAAAATATTAATATCTTAAA-TATTAAT-ATTAA-ATTAT-A--AATA-T-AATTATTAAT
3853177 ATTTAAAAAATAAAAAATAATCATAATAATATTT-AATTA
58 ATTTAAAAAATAAAAAATAATCATAATAATATTTAAATTA
3853216 TAAATAAAATATTAATATCTTATAATATTAATAATTAAATTATAAATATAA-TATTAATATTTAA
1 TAAATAAAATATTAATATCTTA-AATATTAAT-ATTAAATTATAAATATAATTATTAATATTTAA
*
3853280 AAAAT-AAAAATAGATAATAATATATAT
64 AAAATAAAAAATA-ATCATAATA-ATAT
3853307 AAAAAGGATA
Statistics
Matches: 166, Mismatches: 15, Indels: 28
0.79 0.07 0.13
Matches are distributed among these distances:
96 7 0.04
97 26 0.16
98 9 0.05
99 8 0.05
100 24 0.14
101 4 0.02
102 2 0.01
103 25 0.15
104 36 0.22
105 6 0.04
106 4 0.02
107 15 0.09
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (97 bp):
TAAATAAAATATTAATATCTTAAATATTAATATTAAATTATAAATATAATTATTAATATTTAAAA
AATAAAAAATAATCATAATAATATTTAAATTA
Found at i:3853286 original size:26 final size:26
Alignment explanation
Indices: 3853236--3853311 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
3853226 ATTAATATCT
* **
3853236 TATAATATTAATAATTAAATTATAAA
1 TATAATATTAATATTTAAAAAATAAA
3853262 TATAATATTAATATTTAAAAAATAAA
1 TATAATATTAATATTTAAAAAATAAA
* * *
3853288 AATAGATAATAATATATATAAAAA
1 TATA-ATATTAATATTTA-AAAAA
3853312 GGATATTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 26 0.62
27 11 0.26
28 5 0.12
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (26 bp):
TATAATATTAATATTTAAAAAATAAA
Found at i:3853310 original size:27 final size:26
Alignment explanation
Indices: 3853257--3853311 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
3853247 TAATTAAATT
* * *
3853257 ATAAATATAATATTAATATTTAAAAA
1 ATAAAAATAATAATAATATATAAAAA
3853283 ATAAAAATAGATAATAATATATATAAAA
1 ATAAAAATA-ATAATAATATATA-AAAA
3853311 A
1 A
3853312 GGATATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 8 0.33
27 11 0.46
28 5 0.21
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (26 bp):
ATAAAAATAATAATAATATATAAAAA
Found at i:3862132 original size:48 final size:48
Alignment explanation
Indices: 3862076--3862171 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
3862066 CCACCTGATG
3862076 AGTCATAACTTTTTTCTCTCGTCTTTTTTCCCAAAAACAAATTGCACT
1 AGTCATAACTTTTTTCTCTCGTCTTTTTTCCCAAAAACAAATTGCACT
3862124 AGTCATAACTTTTTTCTCTCGTCTTTTTTCCCAAAAACAAATTGCACT
1 AGTCATAACTTTTTTCTCTCGTCTTTTTTCCCAAAAACAAATTGCACT
3862172 TGTTGAGGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.27, C:0.25, G:0.06, T:0.42
Consensus pattern (48 bp):
AGTCATAACTTTTTTCTCTCGTCTTTTTTCCCAAAAACAAATTGCACT
Found at i:3866680 original size:13 final size:14
Alignment explanation
Indices: 3866638--3866698 Score: 56
Period size: 13 Copynumber: 4.3 Consensus size: 14
3866628 TGATTTTTGA
*
3866638 AATTTTTTATATATT
1 AATTTTTTATA-AAT
3866653 ATATATTTTT-T-AAT
1 A-AT-TTTTTATAAAT
3866667 AATTTTTTA-AAAT
1 AATTTTTTATAAAT
3866680 AATTTTTTATTAAAT
1 AATTTTTTA-TAAAT
3866695 AATT
1 AATT
3866699 AATATAATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
12 5 0.13
13 14 0.36
14 3 0.08
15 9 0.23
16 3 0.08
17 5 0.13
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
AATTTTTTATAAAT
Found at i:3867055 original size:15 final size:16
Alignment explanation
Indices: 3867035--3867068 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3867025 TGTTATGCGG
*
3867035 ATTTT-ATTTTTAATA
1 ATTTTAATTTTTAAAA
3867050 ATTTTAATTTTTAAAA
1 ATTTTAATTTTTAAAA
3867066 ATT
1 ATT
3867069 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTAATTTTTAAAA
Found at i:3873066 original size:36 final size:36
Alignment explanation
Indices: 3873025--3873111 Score: 95
Period size: 36 Copynumber: 2.4 Consensus size: 36
3873015 AGTATGGATA
*
3873025 ATTAACTCCATGTACTGACTTTAACTCAAATAATGG
1 ATTAACTCCATGTACTGACTTTAAATCAAATAATGG
* * * * * *
3873061 ATTAACTTCTTATGCTTACTTTAAATCAAATGATGG
1 ATTAACTCCATGTACTGACTTTAAATCAAATAATGG
3873097 -TTAACTCCATAGTAC
1 ATTAACTCCAT-GTAC
3873112 ACGTAGATTA
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
35 8 0.21
36 31 0.79
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.37
Consensus pattern (36 bp):
ATTAACTCCATGTACTGACTTTAAATCAAATAATGG
Found at i:3877491 original size:21 final size:19
Alignment explanation
Indices: 3877455--3877495 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
3877445 ATATGTTAAG
3877455 TAGTTAATTTAAGTTATTT
1 TAGTTAATTTAAGTTATTT
*
3877474 TAGTTAAATTTTATGTTATTT
1 TAGTT-AA-TTTAAGTTATTT
3877495 T
1 T
3877496 GTTTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 2 0.11
21 12 0.63
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (19 bp):
TAGTTAATTTAAGTTATTT
Found at i:3883409 original size:46 final size:46
Alignment explanation
Indices: 3883332--3883446 Score: 144
Period size: 46 Copynumber: 2.5 Consensus size: 46
3883322 GTCTGTTTGT
* * * *
3883332 ATAAATATGTGAGTAAATAATAATTAAGGGTATTTTTAGTAT-TTGGG
1 ATAAATATGTGATTAAATTAT-ATGAAGGGTAATTTTA-TATGTTGGG
*
3883379 ATAAATATGTGATTAAATTATATGAAGGGTAATTTTATCTGTTGGG
1 ATAAATATGTGATTAAATTATATGAAGGGTAATTTTATATGTTGGG
3883425 ATAAATATGT-ATTTAAATTATA
1 ATAAATATGTGA-TTAAATTATA
3883447 ATCAAGATAA
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
45 3 0.05
46 39 0.64
47 19 0.31
ACGTcount: A:0.39, C:0.01, G:0.18, T:0.42
Consensus pattern (46 bp):
ATAAATATGTGATTAAATTATATGAAGGGTAATTTTATATGTTGGG
Found at i:3883458 original size:46 final size:47
Alignment explanation
Indices: 3883268--3883462 Score: 182
Period size: 47 Copynumber: 4.2 Consensus size: 47
3883258 TTAACCAACA
* ** * * * *
3883268 TAATTTTATCTTTTGACATAAATATGTAATAAAAATATAATCAAAGG
1 TAATTTTATCTGTTGGGATAAATATGTGATTAAATTATAATCAAGGG
* * * * * * *
3883315 TTATTTTGTCTGTTTGTATAAATATGTGAGTAAATAATAATTAAGGG
1 TAATTTTATCTGTTGGGATAAATATGTGATTAAATTATAATCAAGGG
* * *
3883362 TATTTTTAGTAT-TTGGGATAAATATGTGATTAAATTAT-ATGAAGGG
1 TAATTTTA-TCTGTTGGGATAAATATGTGATTAAATTATAATCAAGGG
*
3883408 TAATTTTATCTGTTGGGATAAATATGT-ATTTAAATTATAATCAA-GA
1 TAATTTTATCTGTTGGGATAAATATGTGA-TTAAATTATAATCAAGGG
3883454 TAATTTTAT
1 TAATTTTAT
3883463 TTTTTATAAA
Statistics
Matches: 118, Mismatches: 26, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
45 3 0.03
46 48 0.41
47 65 0.55
48 2 0.02
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (47 bp):
TAATTTTATCTGTTGGGATAAATATGTGATTAAATTATAATCAAGGG
Found at i:3884578 original size:18 final size:19
Alignment explanation
Indices: 3884553--3884599 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
3884543 GCTGGTTTTA
3884553 CCTTATTAGTATTTCTTT-
1 CCTTATTAGTATTTCTTTG
* * *
3884571 CTTTATTATTATTTTTTTG
1 CCTTATTAGTATTTCTTTG
3884590 CCTTATTAGT
1 CCTTATTAGT
3884600 TAGTTGACAG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.17, C:0.13, G:0.06, T:0.64
Consensus pattern (19 bp):
CCTTATTAGTATTTCTTTG
Found at i:3899642 original size:2 final size:2
Alignment explanation
Indices: 3899637--3899664 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3899627 AGTGTGTGTG
3899637 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3899665 ATGTAGGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3900608 original size:25 final size:27
Alignment explanation
Indices: 3900575--3900627 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
3900565 TTCGGCTTAT
*
3900575 TTTATTAATA-ATTATTAAAAT-TTAA
1 TTTAGTAATACATTATTAAAATATTAA
*
3900600 TTTAGTAATACATTTTTAAAATATTAA
1 TTTAGTAATACATTATTAAAATATTAA
3900627 T
1 T
3900628 ATAACTTATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 9 0.38
26 10 0.42
27 5 0.21
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
TTTAGTAATACATTATTAAAATATTAA
Found at i:3901126 original size:2 final size:2
Alignment explanation
Indices: 3901119--3901145 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3901109 GCTCAAAATT
3901119 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3901146 TTTGGTCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3902506 original size:12 final size:12
Alignment explanation
Indices: 3902489--3902529 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
3902479 TCTTAGTTAC
*
3902489 TATATACATACA
1 TATATACATATA
3902501 TATATACATATA
1 TATATACATATA
*
3902513 TATATATATATA
1 TATATACATATA
3902525 TATAT
1 TATAT
3902530 CCACTCTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (12 bp):
TATATACATATA
Found at i:3902515 original size:4 final size:4
Alignment explanation
Indices: 3902489--3902529 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
3902479 TCTTAGTTAC
* * *
3902489 TATA TACA TACA TATA TACA TATA TATA TATA TATA TATA T
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA T
3902530 CCACTCTGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (4 bp):
TATA
Found at i:3904651 original size:18 final size:18
Alignment explanation
Indices: 3904625--3904659 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3904615 CTGTGCTCCA
*
3904625 AATAGGGATGATGACGAG
1 AATAAGGATGATGACGAG
*
3904643 AATAAGGATTATGACGA
1 AATAAGGATGATGACGA
3904660 TGACTAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.06, G:0.31, T:0.20
Consensus pattern (18 bp):
AATAAGGATGATGACGAG
Found at i:3911367 original size:29 final size:27
Alignment explanation
Indices: 3911288--3911389 Score: 89
Period size: 26 Copynumber: 3.6 Consensus size: 27
3911278 TTAAAAAAAT
*
3911288 TTAAATAAATTTTTATTATTTTATTACA
1 TTAAATAAATTTTTA-TATTTTATTAAA
* *
3911316 TTCAATCAAGTTTTTATATTTTTATTTTAAA
1 TTAAAT-AAATTTTTATA-TTTTA--TTAAA
* *
3911347 TTAAATAAAATTTTATATTTT-TTTAA
1 TTAAATAAATTTTTATATTTTATTAAA
* *
3911373 TCAAATAAGTTTTTATA
1 TTAAATAAATTTTTATA
3911390 ACTAATGCAC
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
26 18 0.30
28 7 0.12
29 17 0.28
30 9 0.15
31 9 0.15
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (27 bp):
TTAAATAAATTTTTATATTTTATTAAA
Found at i:3914583 original size:17 final size:17
Alignment explanation
Indices: 3914561--3914603 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
3914551 TTTTCCTACA
3914561 TTATTTT-CTTTTCTTTT
1 TTATTTTGC-TTTCTTTT
3914578 TTATTTTGGCTTTCTTTT
1 TTATTTT-GCTTTCTTTT
3914596 TTATTTTG
1 TTATTTTG
3914604 GATTTCATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.33
18 15 0.62
19 1 0.04
ACGTcount: A:0.07, C:0.09, G:0.07, T:0.77
Consensus pattern (17 bp):
TTATTTTGCTTTCTTTT
Found at i:3914591 original size:18 final size:18
Alignment explanation
Indices: 3914570--3914609 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
3914560 ATTATTTTCT
*
3914570 TTTCTTTTTTATTTTGGC
1 TTTCTTTTTTATTTTGGA
3914588 TTTCTTTTTTATTTTGGA
1 TTTCTTTTTTATTTTGGA
3914606 TTTC
1 TTTC
3914610 ATTCTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.07, C:0.10, G:0.10, T:0.72
Consensus pattern (18 bp):
TTTCTTTTTTATTTTGGA
Found at i:3923104 original size:24 final size:24
Alignment explanation
Indices: 3923077--3923125 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
3923067 TAGAATAAAG
**
3923077 TAAGAGTTCTCTTTTATTTAGGAA
1 TAAGAGTTCTAGTTTATTTAGGAA
*
3923101 TAAGAGTTTTAGTTTATTTAGGAA
1 TAAGAGTTCTAGTTTATTTAGGAA
3923125 T
1 T
3923126 GGTAGGGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.47
Consensus pattern (24 bp):
TAAGAGTTCTAGTTTATTTAGGAA
Done.